Archaea, Eukaryotes and the evolution of DNA replication complexes

The relationship between bacteria, archaea and eukaryotes is an interesting one, and made slightly harder to approach as people tend to lump archaea and bacteria into the one grouping of 'prokaryotes' which is not much more than a scientific word for "blobs I don't care about". Delving deeper into the biochemistry of all three superkingdoms shows that while the metabolic pathways used by archaea are more similar to those in bacteria, their core DNA processes (such as replication and protein synthesis) are more similar to the processes in eukaryotes. (I talk more about the distinction between the three superkingdoms here)

There was an interesting paper in PLoS ONE lately that was looking at the evolution of DNA replication complexes in archaea, and seeing as this blog has been rather heavily bacteria-biased (i.e I haven't talked about archaea for a while) I decided to take a look at it. They were focussing on three main complexes that help in DNA replication and are found in both archaea and eukaryotes: proliferating cell nuclear antigen (PCNA), replication factor C (RFC), and the minichromosome maintenance (MCM) complex. Bacteria do use corresponding proteins, but they are far more distantly related.

Schematic of the structure and subunits of the three complexes.

The MCM complex is thought to act as a helicase; unwinding the two DNA strands to allow them to split in two to be replicated. The PCNA and RCF are known as the clamp and clamp loader and help to attach the RNA primer for replication to the Polymerase, which uses the primer to start replicating the DNA.

All of these three complexes consist of separate subunits, which are almost identical. PCNA, for example, is a trimer (in the diagram above each subunit is a separate colour). In eukaryotes these the subunits are identical, but in archaea variations are found between them. This general pattern, that subunit composition was far more variable within the archaea, was found in all three of the complexes. This method of gene duplication followed by gene modification to create two different proteins is an important one for evolution, and in the case of DNA replication it seems to have been exploited far more in archaea than in eukaryotes.

Changing some subunits also allows these complexes to carry out different tasks. It's been suggested that for some archaea there may be a functional difference between PCNA with all subunits the same (homotrimers) and PCAN with differing subunits (a heterotrimer). This allows multiple functions to be generated through simple DNA duplications - although all the functions are likely to relate to DNA replication in some way.

This brings forth the interesting point of view that the truly 'ancestral' forms of these genes and proteins may be more like the proteins seen in the eukaryotes rather than the archaea! Archaea (and bacteria) can tolerate a lot more genetic change than eukaryotes can, and have a far shorter generation time, allowing them to change and evolve more quickly than the larger, less genetically mutable eukaryotes. On the other hand the lack of change and high level of conservation in eukaryotes means that the complexes remain very similar to those of the ancestral eukaryote from which they evolved. They may even be closer to the forms found in the last common ancestor between eukaryotes and archaea, before the eukaryotes gained a nucleus and became unable to share genes with the surrounding organisms.

3 comments:

Quick comment RE 'prokaryotes': Some of us use the term because we believe 'eubacteria' are actually paraphyletic, which Archaea and Eukarya branching within them... it may be a minority view, but IMO, no less plausible than the dominant "Eubacteria are holophyletic and sister to Arch+Euk" view; in fact, makes a lot more sense.

@Psi: prokaryotes is a very handy word to use, because everyone knows what it means. I use it quite often myself, even though I'm not sure I believe that it is a true taxonomic grouping.

@Lucas: Thanks for the link, that looks like an interesting paper (i remember doing some work on Wolbachia in first year). The last statement was a bit throwaway to be honest, I needed to finish the post off before a party and LUCA seemed a good way to do it.